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| author | Pjotr Prins | 2023-12-02 16:45:55 -0600 |
|---|---|---|
| committer | Pjotr Prins | 2023-12-02 16:45:55 -0600 |
| commit | 8fb091769b6b01d476b45943bac54a26a8923573 (patch) | |
| tree | 94569831fcfccb3680dfe47cff41efb01c53278b /gn/runner/gemma.scm | |
| parent | 186da1d636f88421d1bbca0033e2d99a3b15e6cd (diff) | |
| download | gn-guile-8fb091769b6b01d476b45943bac54a26a8923573.tar.gz | |
Run gemma
Diffstat (limited to 'gn/runner/gemma.scm')
| -rw-r--r-- | gn/runner/gemma.scm | 20 |
1 files changed, 14 insertions, 6 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 67dae54..ff70f57 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -23,14 +23,22 @@ ;; ---- write phenotype file (call-with-output-file "pheno.txt" (lambda (port) - (write 12 port) - (newline port) - (write "HELLO" port) - )) + (for-each (lambda (ind) + (begin + (let* [(value (assoc-ref traits ind)) + (outvalue (if value + value + "NA"))] + (display outvalue) + (newline) + (display outvalue port) + (newline port)))) + bxd-inds))) + ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm ;; ---- to start GEMMA precompute inside container - ;; env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm + ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm ;; --- First we compute K - (system (string-append "env GEMMA_COMMAND=/gemma/bin/gemma /gemma-wrapper/bin/gemma-wrapper --debug -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) + (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) ) |